Disposition Sequence

1library(yamaa)23ds <- yamaa_domain("spec.yaml")$output4ds

1import yamaa23ds = yamaa.yamaa_domain("spec.yaml").output4ds

1# Reference solution for the yamaa benchmark sdtm-ds-sequence (R track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67library(dplyr, warn.conflicts = FALSE)8library(readr)9library(stringr)1011ds_raw <- read_csv(12  "/app/input/ds_raw.csv",13  col_types = cols(.default = col_character())14)1516complete_date <- function(x) {17  x <- str_trim(x)18  if (is.na(x) || x == "") {19    return(as.Date(NA))20  }21  parts <- str_split(x, "-", simplify = TRUE)22  n <- ncol(parts)23  if (n == 3 && nchar(parts[1]) == 4) {24    return(suppressWarnings(as.Date(x)))25  }26  if (n == 2 && nchar(parts[1]) == 4) {27    y <- suppressWarnings(as.integer(parts[1]))28    m <- suppressWarnings(as.integer(parts[2]))29    if (is.na(y) || is.na(m) || m < 1 || m > 12) {30      return(as.Date(NA))31    }32    return(suppressWarnings(as.Date(sprintf("%04d-%02d-15", y, m))))33  }34  if (n == 1 && nchar(x) == 4) {35    y <- suppressWarnings(as.integer(x))36    if (is.na(y)) {37      return(as.Date(NA))38    }39    return(suppressWarnings(as.Date(sprintf("%04d-06-15", y))))40  }41  as.Date(NA)42}4344ds <- ds_raw |>45  rowwise() |>46  mutate(47    DOMAIN = "DS",48    STUDYID = STUDY,49    USUBJID = PATNUM,50    DSCAT = ifelse(DSDECOD == "RANDOMIZED", "PROTOCOL MILESTONE", "DISPOSITION EVENT"),51    DSDTC = complete_date(DSDTCOL)52  ) |>53  ungroup() |>54  arrange(USUBJID, DSDTC, DSDECOD) |>55  group_by(USUBJID) |>56  mutate(DSSEQ = row_number()) |>57  ungroup() |>58  select(DOMAIN, STUDYID, USUBJID, DSSEQ, DSDECOD, DSCAT, DSDTC)5960dir.create("/app/output", showWarnings = FALSE)61write_csv(ds, "/app/output/ds.csv", na = "")

1# Reference solution for the yamaa benchmark sdtm-ds-sequence (Python track).2#3# Written from the benchmark's full prompt and its inputs alone, as an agent4# would write it. Harbor's oracle agent runs it to check that the prompt can5# be solved and that the grader scores a correct answer 1.67from pathlib import Path89import polars as pl101112def complete_date(raw: str | None) -> str | None:13    if raw is None:14        return None15    s = raw.strip()16    if s == "":17        return None18    parts = s.split("-")19    try:20        if len(parts) == 3:21            y, m, d = int(parts[0]), int(parts[1]), int(parts[2])22            return f"{y:04d}-{m:02d}-{d:02d}" if len(parts[0]) == 4 else None23        if len(parts) == 2 and len(parts[0]) == 4:24            y, m = int(parts[0]), int(parts[1])25            if 1 <= m <= 12:26                return f"{y:04d}-{m:02d}-15"27            return None28        if len(parts) == 1 and len(s) == 4:29            y = int(s)30            return f"{y:04d}-06-15"31        return None32    except ValueError:33        return None343536ds_raw = pl.read_csv("/app/input/ds_raw.csv", infer_schema=False)3738records: list[dict] = []39for row in ds_raw.to_dicts():40    study = row["STUDY"]41    pat = row["PATNUM"]42    decod = row["DSDECOD"]43    raw = row["DSDTCOL"]44    completed = complete_date(raw)45    # Validate the completed date parses.46    check = pl.DataFrame({"d": [completed]}).with_columns(47        pl.col("d").str.to_date(strict=False).alias("dt")48    )["dt"][0]49    if check is None:50        completed = None51    dscat = "PROTOCOL MILESTONE" if decod == "RANDOMIZED" else "DISPOSITION EVENT"52    records.append(53        {54            "STUDYID": study,55            "USUBJID": pat,56            "DSDECOD": decod,57            "DSCAT": dscat,58            "DSDTC": completed,59        }60    )6162ds = pl.DataFrame(63    records,64    schema={65        "STUDYID": pl.String,66        "USUBJID": pl.String,67        "DSDECOD": pl.String,68        "DSCAT": pl.String,69        "DSDTC": pl.String,70    },71).with_columns(DOMAIN=pl.lit("DS"), DSDTC_DT=pl.col("DSDTC").str.to_date(strict=False))7273ds = (74    ds.sort(["USUBJID", "DSDTC_DT", "DSDECOD"], nulls_last=True)75    .with_columns(DSSEQ=pl.col("USUBJID").cum_count().over("USUBJID"))76    .with_columns(DSSEQ=pl.col("DSSEQ").cast(pl.Int64))77    .select("DOMAIN", "STUDYID", "USUBJID", "DSSEQ", "DSDECOD", "DSCAT", "DSDTC")78)7980Path("/app/output").mkdir(exist_ok=True)81ds.write_csv("/app/output/ds.csv")

1/* opensas reference solution for the yamaa benchmark sdtm-ds-sequence.2   Reads the benchmark inputs and derives the requested output.3   Execute with the existing opensas runtime: opensas /app/output/result.sas. */45data ds_raw;6  length STUDY PATNUM INSTANCE DSDECOD DSDTCOL $1024;7  infile "/app/input/ds_raw.csv" dsd dlm="," firstobs=2 truncover lrecl=32767;8  input STUDY : $char1024. PATNUM : $char1024. INSTANCE : $char1024. DSDECOD : $char1024. DSDTCOL : $char1024.;9run;1011data prepared; set ds_raw; length DOMAIN $2 STUDYID USUBJID DSCAT DSDTC $1024; DOMAIN='DS'; D=.; DSDTC=''; STUDYID=STUDY; USUBJID=PATNUM;12if DSDECOD='RANDOMIZED' then DSCAT='PROTOCOL MILESTONE'; else DSCAT='DISPOSITION EVENT';13if lengthn(DSDTCOL)=10 then D=input(DSDTCOL,?? yymmdd10.); else if lengthn(DSDTCOL)=7 then D=input(cats(DSDTCOL,'-15'),?? yymmdd10.); else if lengthn(DSDTCOL)=4 then D=input(cats(DSDTCOL,'-06-15'),?? yymmdd10.);14if not missing(D) then DSDTC=put(D,yymmdd10.); NODATE=missing(D); run;15proc sort data=prepared; by STUDYID USUBJID NODATE D; run;16data result; set prepared; by STUDYID USUBJID; retain DSSEQ;17  if first.USUBJID then DSSEQ=0;18  DSSEQ+1;19run;2021proc sql;22  create table final as select DOMAIN, STUDYID, USUBJID, DSSEQ, DSDECOD, DSCAT, DSDTC from result;23quit;24proc export data=final outfile="/app/output/ds.csv" dbms=csv replace; run;